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<div class="toc">
 <h3>文章目录</h3>
 <ul><li><ul><li><a href="#_1">导读</a></li><li><a href="#_5">原理</a></li><li><a href="#LDA_score_11">LDA score计算</a></li><li><a href="#_113">安装</a></li><li><a href="#_138">分析</a></li><li><ul><li><a href="#_139">文件输入格式</a></li><li><a href="#_153">数据格式转换</a></li><li><a href="#lefse_202">lefse分析</a></li><li><a href="#lefse_257">绘制lefse结果图</a></li><li><a href="#_314">绘制特征条形图</a></li><li><a href="#_380">绘制系统发育树图</a></li></ul>
   </li><li><a href="#_462">参考资料</a></li></ul>
 </li></ul>
</div>
<p></p> 
<h2><a id="_1"></a>导读</h2> 
<ul><li>LEfSe&#xff08;Linear discriminant analysis Effect Size&#xff09;通过将用于统计显着性的标准检验与编码生物一致性和效果相关性的检验相结合&#xff0c;确定最有可能解释类别之间差异的特征。</li><li>LEfSe分析可以实现多个分组之间的比较&#xff0c;还进行分组比较的内部进行亚组比较分析&#xff0c;从而找到组间在丰度上有显著差异的物种&#xff08;即biomaker&#xff09;。</li></ul> 
<h2><a id="_5"></a>原理</h2> 
<p><img src="https://img-blog.csdnimg.cn/20201014094447340.jpg?x-oss-process&#61;image/watermark,type_ZmFuZ3poZW5naGVpdGk,shadow_10,text_aHR0cHM6Ly9ibG9nLmNzZG4ubmV0L3dlaXhpbl80MjA3Mjc2NQ&#61;&#61;,size_16,color_FFFFFF,t_70#pic_center" alt="在这里插入图片描述" /></p> 
<ol><li>首先在多组样本中采用的非参数检验Kruskal-Wallis秩和检验检测不同分组间丰度差异显著的特征&#xff1b;</li><li>然后在上一步中获得的显著差异特征&#xff0c;用成组的Wilcoxon秩和检验进行组间差异分析&#xff08;若没有亚组&#xff0c;该步跳过&#xff09;&#xff1b;</li><li>最后用线性判别分析&#xff08;LDA&#xff09;对数据进行分类和评估差异显著的物种的影响力&#xff08;即LDA score&#xff09;。</li></ol> 
<h2><a id="LDA_score_11"></a>LDA score计算</h2> 
<p>计算步骤包括&#xff08;详细计算过程看源码&#xff09;&#xff1a;</p> 
<ol><li>拟合lda模型&#xff0c;获取第一特征向量&#xff1b;</li><li>对第一特征向量进行标准化&#xff1b;</li><li>根据标准化后的第一特征向量&#xff0c;计算样本新坐标&#xff1b;</li><li>根据分组信息&#xff0c;计算组间距离&#xff0c;作为效应系数&#xff1b;</li><li>LDA score &#61; 效应系数 * 标准化后特征向量 &#xff1b;</li><li>对LDA score进行log转换。</li></ol> 
<pre><code class="prism language-python"><span class="token keyword">def</span> <span class="token function">test_lda_r</span><span class="token punctuation">(</span>cls<span class="token punctuation">,</span>feats<span class="token punctuation">,</span>cl_sl<span class="token punctuation">,</span>boots<span class="token punctuation">,</span>fract_sample<span class="token punctuation">,</span>lda_th<span class="token punctuation">,</span>tol_min<span class="token punctuation">,</span>nlogs<span class="token punctuation">)</span><span class="token punctuation">:</span>
    fk <span class="token operator">&#61;</span> <span class="token builtin">list</span><span class="token punctuation">(</span>feats<span class="token punctuation">.</span>keys<span class="token punctuation">(</span><span class="token punctuation">)</span><span class="token punctuation">)</span>
    means <span class="token operator">&#61;</span> <span class="token builtin">dict</span><span class="token punctuation">(</span><span class="token punctuation">[</span><span class="token punctuation">(</span>k<span class="token punctuation">,</span><span class="token punctuation">[</span><span class="token punctuation">]</span><span class="token punctuation">)</span> <span class="token keyword">for</span> k <span class="token keyword">in</span> feats<span class="token punctuation">.</span>keys<span class="token punctuation">(</span><span class="token punctuation">)</span><span class="token punctuation">]</span><span class="token punctuation">)</span>
    feats<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span> <span class="token operator">&#61;</span> <span class="token builtin">list</span><span class="token punctuation">(</span>cls<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">)</span>
    clss <span class="token operator">&#61;</span> <span class="token builtin">list</span><span class="token punctuation">(</span><span class="token builtin">set</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">)</span>

    <span class="token keyword">for</span> uu<span class="token punctuation">,</span>k <span class="token keyword">in</span> <span class="token builtin">enumerate</span><span class="token punctuation">(</span>fk<span class="token punctuation">)</span><span class="token punctuation">:</span>
        <span class="token keyword">if</span> k <span class="token operator">&#61;&#61;</span> <span class="token string">&#39;class&#39;</span><span class="token punctuation">:</span>
            <span class="token keyword">continue</span>

        ff <span class="token operator">&#61;</span> <span class="token punctuation">[</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">[</span>i<span class="token punctuation">]</span><span class="token punctuation">,</span>v<span class="token punctuation">)</span> <span class="token keyword">for</span> i<span class="token punctuation">,</span>v <span class="token keyword">in</span> <span class="token builtin">enumerate</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">]</span>

        <span class="token keyword">for</span> c <span class="token keyword">in</span> clss<span class="token punctuation">:</span>
            <span class="token keyword">if</span> <span class="token builtin">len</span><span class="token punctuation">(</span><span class="token builtin">set</span><span class="token punctuation">(</span><span class="token punctuation">[</span><span class="token builtin">float</span><span class="token punctuation">(</span>v<span class="token punctuation">[</span><span class="token number">1</span><span class="token punctuation">]</span><span class="token punctuation">)</span> <span class="token keyword">for</span> v <span class="token keyword">in</span> ff <span class="token keyword">if</span> v<span class="token punctuation">[</span><span class="token number">0</span><span class="token punctuation">]</span> <span class="token operator">&#61;&#61;</span> c<span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">)</span> <span class="token operator">&gt;</span> <span class="token builtin">max</span><span class="token punctuation">(</span><span class="token builtin">float</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">.</span>count<span class="token punctuation">(</span>c<span class="token punctuation">)</span><span class="token punctuation">)</span><span class="token operator">*</span><span class="token number">0.5</span><span class="token punctuation">,</span><span class="token number">4</span><span class="token punctuation">)</span><span class="token punctuation">:</span>
                <span class="token keyword">continue</span>

            <span class="token keyword">for</span> i<span class="token punctuation">,</span>v <span class="token keyword">in</span> <span class="token builtin">enumerate</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">:</span>
                <span class="token keyword">if</span> feats<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">[</span>i<span class="token punctuation">]</span> <span class="token operator">&#61;&#61;</span> c<span class="token punctuation">:</span>
                    feats<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">[</span>i<span class="token punctuation">]</span> <span class="token operator">&#61;</span> math<span class="token punctuation">.</span>fabs<span class="token punctuation">(</span>feats<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">[</span>i<span class="token punctuation">]</span> <span class="token operator">&#43;</span> lrand<span class="token punctuation">.</span>normalvariate<span class="token punctuation">(</span><span class="token number">0.0</span><span class="token punctuation">,</span><span class="token builtin">max</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">[</span>i<span class="token punctuation">]</span><span class="token operator">*</span><span class="token number">0.05</span><span class="token punctuation">,</span><span class="token number">0.01</span><span class="token punctuation">)</span><span class="token punctuation">)</span><span class="token punctuation">)</span>

    rdict <span class="token operator">&#61;</span> <span class="token punctuation">{<!-- --></span><span class="token punctuation">}</span>

    <span class="token keyword">for</span> a<span class="token punctuation">,</span>b <span class="token keyword">in</span> feats<span class="token punctuation">.</span>items<span class="token punctuation">(</span><span class="token punctuation">)</span><span class="token punctuation">:</span>
        <span class="token keyword">if</span> a <span class="token operator">&#61;&#61;</span> <span class="token string">&#39;class&#39;</span> <span class="token operator">or</span> a <span class="token operator">&#61;&#61;</span> <span class="token string">&#39;subclass&#39;</span> <span class="token operator">or</span> a <span class="token operator">&#61;&#61;</span> <span class="token string">&#39;subject&#39;</span><span class="token punctuation">:</span>
            rdict<span class="token punctuation">[</span>a<span class="token punctuation">]</span> <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>StrVector<span class="token punctuation">(</span>b<span class="token punctuation">)</span>
        <span class="token keyword">else</span><span class="token punctuation">:</span>
            rdict<span class="token punctuation">[</span>a<span class="token punctuation">]</span> <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>FloatVector<span class="token punctuation">(</span>b<span class="token punctuation">)</span>

    robjects<span class="token punctuation">.</span>globalenv<span class="token punctuation">[</span><span class="token string">&#34;d&#34;</span><span class="token punctuation">]</span> <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>DataFrame<span class="token punctuation">(</span>rdict<span class="token punctuation">)</span>
    lfk <span class="token operator">&#61;</span> <span class="token builtin">len</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span>fk<span class="token punctuation">[</span><span class="token number">0</span><span class="token punctuation">]</span><span class="token punctuation">]</span><span class="token punctuation">)</span>
    rfk <span class="token operator">&#61;</span> <span class="token builtin">int</span><span class="token punctuation">(</span><span class="token builtin">float</span><span class="token punctuation">(</span><span class="token builtin">len</span><span class="token punctuation">(</span>feats<span class="token punctuation">[</span>fk<span class="token punctuation">[</span><span class="token number">0</span><span class="token punctuation">]</span><span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">)</span><span class="token operator">*</span>fract_sample<span class="token punctuation">)</span>
    f <span class="token operator">&#61;</span> <span class="token string">&#34;class ~ &#34;</span><span class="token operator">&#43;</span>fk<span class="token punctuation">[</span><span class="token number">0</span><span class="token punctuation">]</span>

    <span class="token keyword">for</span> k <span class="token keyword">in</span> fk<span class="token punctuation">[</span><span class="token number">1</span><span class="token punctuation">:</span><span class="token punctuation">]</span><span class="token punctuation">:</span>
        f <span class="token operator">&#43;&#61;</span> <span class="token string">&#34; &#43; &#34;</span> <span class="token operator">&#43;</span> k<span class="token punctuation">.</span>strip<span class="token punctuation">(</span><span class="token punctuation">)</span>

    ncl <span class="token operator">&#61;</span> <span class="token builtin">len</span><span class="token punctuation">(</span><span class="token builtin">set</span><span class="token punctuation">(</span>cls<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">)</span>
    min_cl <span class="token operator">&#61;</span> <span class="token builtin">int</span><span class="token punctuation">(</span><span class="token builtin">float</span><span class="token punctuation">(</span><span class="token builtin">min</span><span class="token punctuation">(</span><span class="token punctuation">[</span>cls<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">.</span>count<span class="token punctuation">(</span>c<span class="token punctuation">)</span> <span class="token keyword">for</span> c <span class="token keyword">in</span> <span class="token builtin">set</span><span class="token punctuation">(</span>cls<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token punctuation">)</span><span class="token operator">*</span>fract_sample<span class="token operator">*</span>fract_sample<span class="token operator">*</span><span class="token number">0.5</span><span class="token punctuation">)</span>
    min_cl <span class="token operator">&#61;</span> <span class="token builtin">max</span><span class="token punctuation">(</span>min_cl<span class="token punctuation">,</span><span class="token number">1</span><span class="token punctuation">)</span>
    pairs <span class="token operator">&#61;</span> <span class="token punctuation">[</span><span class="token punctuation">(</span>a<span class="token punctuation">,</span>b<span class="token punctuation">)</span> <span class="token keyword">for</span> a <span class="token keyword">in</span> <span class="token builtin">set</span><span class="token punctuation">(</span>cls<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">)</span> <span class="token keyword">for</span> b <span class="token keyword">in</span> <span class="token builtin">set</span><span class="token punctuation">(</span>cls<span class="token punctuation">[</span><span class="token string">&#39;class&#39;</span><span class="token punctuation">]</span><span class="token punctuation">)</span> <span class="token keyword">if</span> a <span class="token operator">&gt;</span> b<span class="token punctuation">]</span>

    <span class="token keyword">for</span> k <span class="token keyword">in</span> fk<span class="token punctuation">:</span>
        <span class="token keyword">for</span> i <span class="token keyword">in</span> <span class="token builtin">range</span><span class="token punctuation">(</span>boots<span class="token punctuation">)</span><span class="token punctuation">:</span>
            means<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">.</span>append<span class="token punctuation">(</span><span class="token punctuation">[</span><span class="token punctuation">]</span><span class="token punctuation">)</span>

    <span class="token keyword">for</span> i <span class="token keyword">in</span> <span class="token builtin">range</span><span class="token punctuation">(</span>boots<span class="token punctuation">)</span><span class="token punctuation">:</span>
        <span class="token keyword">for</span> rtmp <span class="token keyword">in</span> <span class="token builtin">range</span><span class="token punctuation">(</span><span class="token number">1000</span><span class="token punctuation">)</span><span class="token punctuation">:</span>
            rand_s <span class="token operator">&#61;</span> <span class="token punctuation">[</span>lrand<span class="token punctuation">.</span>randint<span class="token punctuation">(</span><span class="token number">0</span><span class="token punctuation">,</span>lfk<span class="token operator">-</span><span class="token number">1</span><span class="token punctuation">)</span> <span class="token keyword">for</span> v <span class="token keyword">in</span> <span class="token builtin">range</span><span class="token punctuation">(</span>rfk<span class="token punctuation">)</span><span class="token punctuation">]</span>
            <span class="token keyword">if</span> <span class="token operator">not</span> contast_within_classes_or_few_per_class<span class="token punctuation">(</span>feats<span class="token punctuation">,</span>rand_s<span class="token punctuation">,</span>min_cl<span class="token punctuation">,</span>ncl<span class="token punctuation">)</span><span class="token punctuation">:</span>
                <span class="token keyword">break</span>

        rand_s <span class="token operator">&#61;</span> <span class="token punctuation">[</span>r<span class="token operator">&#43;</span><span class="token number">1</span> <span class="token keyword">for</span> r <span class="token keyword">in</span> rand_s<span class="token punctuation">]</span>
        means<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">[</span>i<span class="token punctuation">]</span> <span class="token operator">&#61;</span> <span class="token punctuation">[</span><span class="token punctuation">]</span>

        <span class="token keyword">for</span> p <span class="token keyword">in</span> pairs<span class="token punctuation">:</span>
            robjects<span class="token punctuation">.</span>globalenv<span class="token punctuation">[</span><span class="token string">&#34;rand_s&#34;</span><span class="token punctuation">]</span> <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>IntVector<span class="token punctuation">(</span>rand_s<span class="token punctuation">)</span>
            robjects<span class="token punctuation">.</span>globalenv<span class="token punctuation">[</span><span class="token string">&#34;sub_d&#34;</span><span class="token punctuation">]</span> <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;d[rand_s,]&#39;</span><span class="token punctuation">)</span>
            z <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;z &lt;- suppressWarnings(lda(as.formula(&#39;</span><span class="token operator">&#43;</span>f<span class="token operator">&#43;</span><span class="token string">&#39;),data&#61;sub_d,tol&#61;&#39;</span><span class="token operator">&#43;</span><span class="token builtin">str</span><span class="token punctuation">(</span>tol_min<span class="token punctuation">)</span><span class="token operator">&#43;</span><span class="token string">&#39;))&#39;</span><span class="token punctuation">)</span>
            robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;w &lt;- z$scaling[,1]&#39;</span><span class="token punctuation">)</span>
            robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;w.unit &lt;- w/sqrt(sum(w^2))&#39;</span><span class="token punctuation">)</span>
            robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;ss &lt;- sub_d[,-match(&#34;class&#34;,colnames(sub_d))]&#39;</span><span class="token punctuation">)</span>

            <span class="token keyword">if</span> <span class="token string">&#39;subclass&#39;</span> <span class="token keyword">in</span> feats<span class="token punctuation">:</span>
                robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;ss &lt;- ss[,-match(&#34;subclass&#34;,colnames(ss))]&#39;</span><span class="token punctuation">)</span>

            <span class="token keyword">if</span> <span class="token string">&#39;subject&#39;</span> <span class="token keyword">in</span> feats<span class="token punctuation">:</span>
                robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;ss &lt;- ss[,-match(&#34;subject&#34;,colnames(ss))]&#39;</span><span class="token punctuation">)</span>

            robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;xy.matrix &lt;- as.matrix(ss)&#39;</span><span class="token punctuation">)</span>
            robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;LD &lt;- xy.matrix%*%w.unit&#39;</span><span class="token punctuation">)</span>
            robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;effect.size &lt;- abs(mean(LD[sub_d[,&#34;class&#34;]&#61;&#61;&#34;&#39;</span><span class="token operator">&#43;</span>p<span class="token punctuation">[</span><span class="token number">0</span><span class="token punctuation">]</span><span class="token operator">&#43;</span><span class="token string">&#39;&#34;]) - mean(LD[sub_d[,&#34;class&#34;]&#61;&#61;&#34;&#39;</span><span class="token operator">&#43;</span>p<span class="token punctuation">[</span><span class="token number">1</span><span class="token punctuation">]</span><span class="token operator">&#43;</span><span class="token string">&#39;&#34;]))&#39;</span><span class="token punctuation">)</span>
            scal <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;wfinal &lt;- w.unit * effect.size&#39;</span><span class="token punctuation">)</span>
            rres <span class="token operator">&#61;</span> robjects<span class="token punctuation">.</span>r<span class="token punctuation">(</span><span class="token string">&#39;mm &lt;- z$means&#39;</span><span class="token punctuation">)</span>
            rowns <span class="token operator">&#61;</span> <span class="token builtin">list</span><span class="token punctuation">(</span>rres<span class="token punctuation">.</span>rownames<span class="token punctuation">)</span>
            lenc <span class="token operator">&#61;</span> <span class="token builtin">len</span><span class="token punctuation">(</span><span class="token builtin">list</span><span class="token punctuation">(</span>rres<span class="token punctuation">.</span>colnames<span class="token punctuation">)</span><span class="token punctuation">)</span>
            coeff <span class="token operator">&#61;</span> <span class="token punctuation">[</span><span class="token builtin">abs</span><span class="token punctuation">(</span><span class="token builtin">float</span><span class="token punctuation">(</span>v<span class="token punctuation">)</span><span class="token punctuation">)</span> <span class="token keyword">if</span> <span class="token operator">not</span> math<span class="token punctuation">.</span>isnan<span class="token punctuation">(</span><span class="token builtin">float</span><span class="token punctuation">(</span>v<span class="token punctuation">)</span><span class="token punctuation">)</span> <span class="token keyword">else</span> <span class="token number">0.0</span> <span class="token keyword">for</span> v <span class="token keyword">in</span> scal<span class="token punctuation">]</span>
            res <span class="token operator">&#61;</span> <span class="token builtin">dict</span><span class="token punctuation">(</span><span class="token punctuation">[</span><span class="token punctuation">(</span>pp<span class="token punctuation">,</span><span class="token punctuation">[</span><span class="token builtin">float</span><span class="token punctuation">(</span>ff<span class="token punctuation">)</span> <span class="token keyword">for</span> ff <span class="token keyword">in</span> rres<span class="token punctuation">.</span>rx<span class="token punctuation">(</span>pp<span class="token punctuation">,</span><span class="token boolean">True</span><span class="token punctuation">)</span><span class="token punctuation">]</span> <span class="token keyword">if</span> pp <span class="token keyword">in</span> rowns <span class="token keyword">else</span> <span class="token punctuation">[</span><span class="token number">0.0</span><span class="token punctuation">]</span><span class="token operator">*</span>lenc <span class="token punctuation">)</span> <span class="token keyword">for</span> pp <span class="token keyword">in</span> <span class="token punctuation">[</span>p<span class="token punctuation">[</span><span class="token number">0</span><span class="token punctuation">]</span><span class="token punctuation">,</span>p<span class="token punctuation">[</span><span class="token number">1</span><span class="token punctuation">]</span><span class="token punctuation">]</span><span class="token punctuation">]</span><span class="token punctuation">)</span>

            <span class="token keyword">for</span> j<span class="token punctuation">,</span>k <span class="token keyword">in</span> <span class="token builtin">enumerate</span><span class="token punctuation">(</span>fk<span class="token punctuation">)</span><span class="token punctuation">:</span>
                gm <span class="token operator">&#61;</span> <span class="token builtin">abs</span><span class="token punctuation">(</span>res<span class="token punctuation">[</span>p<span class="token punctuation">[</span><span class="token number">0</span><span class="token punctuation">]</span><span class="token punctuation">]</span><span class="token punctuation">[</span>j<span class="token punctuation">]</span> <span class="token operator">-</span> res<span class="token punctuation">[</span>p<span class="token punctuation">[</span><span class="token number">1</span><span class="token punctuation">]</span><span class="token punctuation">]</span><span class="token punctuation">[</span>j<span class="token punctuation">]</span><span class="token punctuation">)</span>
                means<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">[</span>i<span class="token punctuation">]</span><span class="token punctuation">.</span>append<span class="token punctuation">(</span><span class="token punctuation">(</span>gm<span class="token operator">&#43;</span>coeff<span class="token punctuation">[</span>j<span class="token punctuation">]</span><span class="token punctuation">)</span><span class="token operator">*</span><span class="token number">0.5</span><span class="token punctuation">)</span>

    res <span class="token operator">&#61;</span> <span class="token punctuation">{<!-- --></span><span class="token punctuation">}</span>

    <span class="token keyword">for</span> k <span class="token keyword">in</span> fk<span class="token punctuation">:</span>
        m <span class="token operator">&#61;</span> <span class="token builtin">max</span><span class="token punctuation">(</span><span class="token punctuation">[</span>numpy<span class="token punctuation">.</span>mean<span class="token punctuation">(</span><span class="token punctuation">[</span>means<span class="token punctuation">[</span>k<span class="token punctuation">]</span><span class="token punctuation">[</span>kk<span class="token punctuation">]</span><span class="token punctuation">[</span>p<span class="token punctuation">]</span> <span class="token keyword">for</span> kk <span class="token keyword">in</span> <span class="token builtin">range</span><span class="token punctuation">(</span>boots<span class="token punctuation">)</span><span class="token punctuation">]</span><span class="token punctuation">)</span> <span class="token keyword">for</span> p <span class="token keyword">in</span> <span class="token builtin">range</span><span class="token punctuation">(</span><span class="token builtin">len</span><span class="token punctuation">(</span>pairs<span class="token punctuation">)</span><span class="token punctuation">)</span><span class="token punctuation">]</span><span class="token punctuation">)</span>
        res<span class="token punctuation">[</span>k<span class="token punctuation">]</span> <span class="token operator">&#61;</span> math<span class="token punctuation">.</span>copysign<span class="token punctuation">(</span><span class="token number">1.0</span><span class="token punctuation">,</span>m<span class="token punctuation">)</span><span class="token operator">*</span>math<span class="token punctuation">.</span>log<span class="token punctuation">(</span><span class="token number">1.0</span><span class="token operator">&#43;</span>math<span class="token punctuation">.</span>fabs<span class="token punctuation">(</span>m<span class="token punctuation">)</span><span class="token punctuation">,</span><span class="token number">10</span><span class="token punctuation">)</span>

    <span class="token keyword">return</span> res<span class="token punctuation">,</span><span class="token builtin">dict</span><span class="token punctuation">(</span><span class="token punctuation">[</span><span class="token punctuation">(</span>k<span class="token punctuation">,</span>x<span class="token punctuation">)</span> <span class="token keyword">for</span> k<span class="token punctuation">,</span>x <span class="token keyword">in</span> res<span class="token punctuation">.</span>items<span class="token punctuation">(</span><span class="token punctuation">)</span> <span class="token keyword">if</span> math<span class="token punctuation">.</span>fabs<span class="token punctuation">(</span>x<span class="token punctuation">)</span> <span class="token operator">&gt;</span> lda_th<span class="token punctuation">]</span><span class="token punctuation">)</span>

</code></pre> 
<h2><a id="_113"></a>安装</h2> 
<pre><code class="prism language-shell"><span class="token comment"># 新建虚拟环境&#xff0c;lefse依赖于python2</span>
conda create -n lefse python<span class="token operator">&#61;</span>2.7

<span class="token comment"># 激活虚拟环境</span>
<span class="token function">source</span> activate lefse

<span class="token comment"># conda安装lefse</span>
conda <span class="token function">install</span> lefse

<span class="token comment"># 退出虚拟环境</span>
<span class="token function">source</span> deactivate
</code></pre> 
<hr /> 
<p>报错&#xff1a;如果是r2py的问题&#xff0c;基本都是python版本的问题。<br /> 解决&#xff1a;虚拟环境中重新安装python2.7&#xff08;推荐&#xff09;。另一种方式是对虚拟环境中的conda降级&#xff0c;之后再进行安装。</p> 
<hr /> 
<p>报错&#xff1a;如果是axis_bgcolor()的问题&#xff0c;那就是matplotlib版本问题。<br /> 解决&#xff1a;虚拟环境中重新安装metaplotlib 2.0版本&#xff0c;<code>conda install matplotlib&#61;2.0</code>&#xff08;推荐&#xff09;。另一种方式是将lefse-plot_cladogam.py文件中的<code>axis_bgcolor()</code>修改为<code>facecolor()</code>。</p> 
<hr /> 
<h2><a id="_138"></a>分析</h2> 
<h3><a id="_139"></a>文件输入格式</h3> 
<p>文本制表符&#xff08;单个Tab&#xff09;分隔的输入文件由特征列表&#xff0c;分类向量和可选的亚组变量和样本ID向量组成。元数据位于前几行&#xff0c;特征矩阵随后。</p> 
<pre><code class="prism language-shell">bodysite                                mucosal         mucosal         mucosal         mucosal         mucosal         non_mucosal     non_mucosal     non_mucosal     non_mucosal     non_mucosal
subsite                                 oral            gut             oral            oral            gut             skin            nasal           skin            ear             nasal
<span class="token function">id</span>                                      1023            1023            1672            1876            1672            159005010       1023            1023            1023            1672
Bacteria                                0.99999         0.99999         0.999993        0.999989        0.999997        0.999927        0.999977        0.999987        0.999997        0.999993
Bacteria<span class="token operator">|</span>Actinobacteria                 0.311037        0.000864363     0.00446132      0.0312045       0.000773642     0.359354        0.761108        0.603002        0.95913         0.753688
Bacteria<span class="token operator">|</span>Bacteroidetes                  0.0689602       0.804293        0.00983343      0.0303561       0.859838        0.0195298       0.0212741       0.145729        0.0115617       0.0114511
Bacteria<span class="token operator">|</span>Firmicutes                     0.494223        0.173411        0.715345        0.813046        0.124552        0.177961        0.189178        0.188964        0.0226835       0.192665
Bacteria<span class="token operator">|</span>Proteobacteria                 0.0914284       0.0180378       0.265664        0.109549        0.00941215      0.430869        0.0225884       0.0532684       0.00512034      0.0365453
Bacteria<span class="token operator">|</span>Firmicutes<span class="token operator">|</span>Clostridia          0.090041        0.170246        0.00483188      0.0465328       0.122702        0.0402301       0.0460614       0.135201        0.0115835       0.0537381
</code></pre> 
<h3><a id="_153"></a>数据格式转换</h3> 
<p>数据分析前需要对数据格式进行转换&#xff0c;原始数据可以为16S那种reads count&#xff0c;也可以是宏基因组相对丰度数据&#xff0c;但需要按照指定格式&#xff0c;行为分组和物种信息&#xff0c;列为样本。<code>-c</code>指定分组行&#xff1b;<code>-s</code>指定亚组行&#xff0c;若没有可以不指定&#xff1b;<code>-u</code>指定样本编号&#xff1b;<code>-o</code>指定归一化后范围&#xff0c;主要针对宏基因组数据&#xff0c;目的是对相对丰度进行放大。</p> 
<pre><code class="prism language-shell">lefse-format_input.py hmp_aerobiosis_small.txt hmp_aerobiosis_small.in -c 1 -s 2 -u 3 -o 1000000
</code></pre> 
<p>详细参数&#xff1a;</p> 
<pre><code class="prism language-shell">usage: lefse-format_input.py <span class="token punctuation">[</span>-h<span class="token punctuation">]</span> <span class="token punctuation">[</span>--output_table OUTPUT_TABLE<span class="token punctuation">]</span> <span class="token punctuation">[</span>-f <span class="token punctuation">{<!-- --></span>c,r<span class="token punctuation">}</span><span class="token punctuation">]</span>
                             <span class="token punctuation">[</span>-c <span class="token punctuation">[</span>1<span class="token punctuation">..</span>n_feats<span class="token punctuation">]</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>-s <span class="token punctuation">[</span>1<span class="token punctuation">..</span>n_feats<span class="token punctuation">]</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>-o float<span class="token punctuation">]</span>
                             <span class="token punctuation">[</span>-u <span class="token punctuation">[</span>1<span class="token punctuation">..</span>n_feats<span class="token punctuation">]</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>-m <span class="token punctuation">{<!-- --></span>f,s<span class="token punctuation">}</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>-n int<span class="token punctuation">]</span>
                             <span class="token punctuation">[</span>-biom_c BIOM_CLASS<span class="token punctuation">]</span> <span class="token punctuation">[</span>-biom_s BIOM_SUBCLASS<span class="token punctuation">]</span>
                             INPUT_FILE OUTPUT_FILE

LEfSe formatting modules

positional arguments:
  INPUT_FILE            the input file, feature hierarchical level can be
                        specified with <span class="token operator">|</span> or <span class="token keyword">.</span> and those symbols must not be
                        present <span class="token keyword">for</span> other reasons <span class="token keyword">in</span> the input file.
  OUTPUT_FILE           the output <span class="token function">file</span> containing the data <span class="token keyword">for</span> LEfSe

optional arguments:
  -h, --help            show this <span class="token function">help</span> message and <span class="token keyword">exit</span>
  --output_table OUTPUT_TABLE
                        the formatted table <span class="token keyword">in</span> txt <span class="token function">format</span>
  -f <span class="token punctuation">{<!-- --></span>c,r<span class="token punctuation">}</span>              <span class="token keyword">set</span> whether the features are on rows <span class="token punctuation">(</span>default<span class="token punctuation">)</span> or on
                        columns
  -c <span class="token punctuation">[</span>1<span class="token punctuation">..</span>n_feats<span class="token punctuation">]</span>       <span class="token keyword">set</span> <span class="token function">which</span> feature use as class <span class="token punctuation">(</span>default 1<span class="token punctuation">)</span>
  -s <span class="token punctuation">[</span>1<span class="token punctuation">..</span>n_feats<span class="token punctuation">]</span>       <span class="token keyword">set</span> <span class="token function">which</span> feature use as subclass <span class="token punctuation">(</span>default -1 meaning
                        no subclass<span class="token punctuation">)</span>
  -o float              <span class="token keyword">set</span> the normalization value <span class="token punctuation">(</span>default -1.0 meaning no
                        normalization<span class="token punctuation">)</span>
  -u <span class="token punctuation">[</span>1<span class="token punctuation">..</span>n_feats<span class="token punctuation">]</span>       <span class="token keyword">set</span> <span class="token function">which</span> feature use as subject <span class="token punctuation">(</span>default -1 meaning
                        no subject<span class="token punctuation">)</span>
  -m <span class="token punctuation">{<!-- --></span>f,s<span class="token punctuation">}</span>              <span class="token keyword">set</span> the policy to adopt with missin values: f removes
                        the features with missing values, s removes samples
                        with missing values <span class="token punctuation">(</span>default f<span class="token punctuation">)</span>
  -n int                <span class="token keyword">set</span> the minimum cardinality of each subclass
                        <span class="token punctuation">(</span>subclasses with low cardinalities will be grouped
                        together, <span class="token keyword">if</span> the cardinality is still low, no pairwise
                        comparison will be performed with them<span class="token punctuation">)</span>
  -biom_c BIOM_CLASS    For biom input files: Set <span class="token function">which</span> feature use as class
  -biom_s BIOM_SUBCLASS
                        For biom input files: <span class="token keyword">set</span> <span class="token function">which</span> feature use as
                        subclass

</code></pre> 
<h3><a id="lefse_202"></a>lefse分析</h3> 
<p>转换格式后&#xff0c;可以进行lefse差异分析。需要指定输入和输出文件。还可以通过<code>-a</code>指定组间比较检验水准阈值&#xff0c;<code>-w</code>指定成组比较检验水准阈值&#xff0c;<code>-l</code>指定lda score阈值。除了可以选择lda&#xff0c;还可以选择svm进行分析。</p> 
<pre><code class="prism language-shell">run_lefse.py hmp_aerobiosis_small.in hmp_aerobiosis_small.res
</code></pre> 
<p>详细参数&#xff1a;</p> 
<pre><code class="prism language-shell">usage: run_lefse.py <span class="token punctuation">[</span>-h<span class="token punctuation">]</span> <span class="token punctuation">[</span>-o str<span class="token punctuation">]</span> <span class="token punctuation">[</span>-a float<span class="token punctuation">]</span> <span class="token punctuation">[</span>-w float<span class="token punctuation">]</span> <span class="token punctuation">[</span>-l float<span class="token punctuation">]</span>
                    <span class="token punctuation">[</span>--nlogs int<span class="token punctuation">]</span> <span class="token punctuation">[</span>--verbose int<span class="token punctuation">]</span> <span class="token punctuation">[</span>--wilc int<span class="token punctuation">]</span> <span class="token punctuation">[</span>-r str<span class="token punctuation">]</span>
                    <span class="token punctuation">[</span>--svm_norm int<span class="token punctuation">]</span> <span class="token punctuation">[</span>-b int<span class="token punctuation">]</span> <span class="token punctuation">[</span>-e int<span class="token punctuation">]</span> <span class="token punctuation">[</span>-c int<span class="token punctuation">]</span> <span class="token punctuation">[</span>-f float<span class="token punctuation">]</span>
                    <span class="token punctuation">[</span>-s <span class="token punctuation">{<!-- --></span>0,1,2<span class="token punctuation">}</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>--min_c int<span class="token punctuation">]</span> <span class="token punctuation">[</span>-t str<span class="token punctuation">]</span> <span class="token punctuation">[</span>-y <span class="token punctuation">{<!-- --></span>0,1<span class="token punctuation">}</span><span class="token punctuation">]</span>
                    INPUT_FILE OUTPUT_FILE

LEfSe 1.0

positional arguments:
  INPUT_FILE      the input <span class="token function">file</span>
  OUTPUT_FILE     the output <span class="token function">file</span> containing the data <span class="token keyword">for</span> the visualization
                  module

optional arguments:
  -h, --help      show this <span class="token function">help</span> message and <span class="token keyword">exit</span>
  -o str          <span class="token keyword">set</span> the <span class="token function">file</span> <span class="token keyword">for</span> exporting the result <span class="token punctuation">(</span>only concise textual
                  form<span class="token punctuation">)</span>
  -a float        <span class="token keyword">set</span> the alpha value <span class="token keyword">for</span> the Anova <span class="token function">test</span> <span class="token punctuation">(</span>default 0.05<span class="token punctuation">)</span>
  -w float        <span class="token keyword">set</span> the alpha value <span class="token keyword">for</span> the Wilcoxon <span class="token function">test</span> <span class="token punctuation">(</span>default 0.05<span class="token punctuation">)</span>
  -l float        <span class="token keyword">set</span> the threshold on the absolute value of the logarithmic
                  LDA score <span class="token punctuation">(</span>default 2.0<span class="token punctuation">)</span>
  --nlogs int     max log ingluence of LDA coeff
  --verbose int   verbose execution <span class="token punctuation">(</span>default 0<span class="token punctuation">)</span>
  --wilc int      wheter to perform the Wicoxon step <span class="token punctuation">(</span>default 1<span class="token punctuation">)</span>
  -r str          <span class="token keyword">select</span> LDA or SVM <span class="token keyword">for</span> effect size <span class="token punctuation">(</span>default LDA<span class="token punctuation">)</span>
  --svm_norm int  whether to normalize the data <span class="token keyword">in</span> <span class="token punctuation">[</span>0,1<span class="token punctuation">]</span> <span class="token keyword">for</span> SVM feature
                  waiting <span class="token punctuation">(</span>default 1 strongly suggested<span class="token punctuation">)</span>
  -b int          <span class="token keyword">set</span> the number of bootstrap iteration <span class="token keyword">for</span> LDA <span class="token punctuation">(</span>default 30<span class="token punctuation">)</span>
  -e int          <span class="token keyword">set</span> whether perform the wilcoxon <span class="token function">test</span> only among the
                  subclasses with the same name <span class="token punctuation">(</span>default 0<span class="token punctuation">)</span>
  -c int          <span class="token keyword">set</span> whether perform the wilcoxon <span class="token function">test</span> ing the Curtis&#39;s
                  approach <span class="token punctuation">[</span>BETA VERSION<span class="token punctuation">]</span> <span class="token punctuation">(</span>default 0<span class="token punctuation">)</span>
  -f float        <span class="token keyword">set</span> the subsampling fraction value <span class="token keyword">for</span> each bootstrap
                  iteration <span class="token punctuation">(</span>default 0.66666<span class="token punctuation">)</span>
  -s <span class="token punctuation">{<!-- --></span>0,1,2<span class="token punctuation">}</span>      <span class="token keyword">set</span> the multiple testing correction options. 0 no correction
                  <span class="token punctuation">(</span>more strict, default<span class="token punctuation">)</span>, 1 correction <span class="token keyword">for</span> independent
                  comparisons, 2 correction <span class="token keyword">for</span> independent comparison
  --min_c int     minimum number of samples per subclass <span class="token keyword">for</span> performing
                  wilcoxon <span class="token function">test</span> <span class="token punctuation">(</span>default 10<span class="token punctuation">)</span>
  -t str          <span class="token keyword">set</span> the title of the analysis <span class="token punctuation">(</span>default input <span class="token function">file</span> without
                  extension<span class="token punctuation">)</span>
  -y <span class="token punctuation">{<!-- --></span>0,1<span class="token punctuation">}</span>        <span class="token punctuation">(</span>for multiclass tasks<span class="token punctuation">)</span> <span class="token keyword">set</span> whether the <span class="token function">test</span> is performed <span class="token keyword">in</span>
                  a one-against-one <span class="token punctuation">(</span> 1 - <span class="token function">more</span> strict<span class="token operator">!</span><span class="token punctuation">)</span> or <span class="token keyword">in</span> a one-against-
                  all setting <span class="token punctuation">(</span> 0 - <span class="token function">less</span> strict<span class="token punctuation">)</span> <span class="token punctuation">(</span>default 0<span class="token punctuation">)</span>

</code></pre> 
<h3><a id="lefse_257"></a>绘制lefse结果图</h3> 
<p>将lefse分析结果绘图。可以根据需求指定绘图格式。</p> 
<pre><code class="prism language-shell">lefse-plot_res.py hmp_aerobiosis_small.res hmp_aerobiosis_small.png
</code></pre> 
<p>详细参数&#xff1a;</p> 
<pre><code class="prism language-shell">usage: lefse-plot_res.py <span class="token punctuation">[</span>-h<span class="token punctuation">]</span> <span class="token punctuation">[</span>--feature_font_size FEATURE_FONT_SIZE<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--format <span class="token punctuation">{<!-- --></span>png,svg,pdf<span class="token punctuation">}</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>--dpi DPI<span class="token punctuation">]</span> <span class="token punctuation">[</span>--title TITLE<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--title_font_size TITLE_FONT_SIZE<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--class_legend_font_size CLASS_LEGEND_FONT_SIZE<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--width WIDTH<span class="token punctuation">]</span> <span class="token punctuation">[</span>--height HEIGHT<span class="token punctuation">]</span> <span class="token punctuation">[</span>--left_space LS<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--right_space RS<span class="token punctuation">]</span> <span class="token punctuation">[</span>--orientation <span class="token punctuation">{<!-- --></span>h,v<span class="token punctuation">}</span><span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--autoscale <span class="token punctuation">{<!-- --></span>0,1<span class="token punctuation">}</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>--background_color <span class="token punctuation">{<!-- --></span>k,w<span class="token punctuation">}</span><span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--subclades N_SCL<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--max_feature_len MAX_FEATURE_LEN<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--all_feats ALL_FEATS<span class="token punctuation">]</span> <span class="token punctuation">[</span>--otu_only<span class="token punctuation">]</span>
                         <span class="token punctuation">[</span>--report_features<span class="token punctuation">]</span>
                         INPUT_FILE OUTPUT_FILE

Plot results

positional arguments:
  INPUT_FILE            tab delimited input <span class="token function">file</span>
  OUTPUT_FILE           the <span class="token function">file</span> <span class="token keyword">for</span> the output image

optional arguments:
  -h, --help            show this <span class="token function">help</span> message and <span class="token keyword">exit</span>
  --feature_font_size FEATURE_FONT_SIZE
                        the <span class="token function">file</span> <span class="token keyword">for</span> the output image
  --format <span class="token punctuation">{<!-- --></span>png,svg,pdf<span class="token punctuation">}</span>
                        the <span class="token function">format</span> <span class="token keyword">for</span> the output <span class="token function">file</span>
  --dpi DPI
  --title TITLE
  --title_font_size TITLE_FONT_SIZE
  --class_legend_font_size CLASS_LEGEND_FONT_SIZE
  --width WIDTH
  --height HEIGHT       only <span class="token keyword">for</span> vertical histograms
  --left_space LS
  --right_space RS
  --orientation <span class="token punctuation">{<!-- --></span>h,v<span class="token punctuation">}</span>
  --autoscale <span class="token punctuation">{<!-- --></span>0,1<span class="token punctuation">}</span>
  --background_color <span class="token punctuation">{<!-- --></span>k,w<span class="token punctuation">}</span>
                        <span class="token keyword">set</span> the color of the background
  --subclades N_SCL     number of label levels to be dislayed <span class="token punctuation">(</span>starting from
                        the leaves, -1 means all the levels, 1 is default <span class="token punctuation">)</span>
  --max_feature_len MAX_FEATURE_LEN
                        Maximum length of feature strings <span class="token punctuation">(</span>def 60<span class="token punctuation">)</span>
  --all_feats ALL_FEATS
  --otu_only            Plot only species resolved OTUs <span class="token punctuation">(</span>as opposed to all
                        levels<span class="token punctuation">)</span>
  --report_features     Report important features to STDOUT

</code></pre> 
<h3><a id="_314"></a>绘制特征条形图</h3> 
<p>另外&#xff0c;可以分别对指定的物种&#xff0c;或者所以差异物种绘制条形图。</p> 
<pre><code class="prism language-shell"><span class="token comment"># 单个特征</span>
lefse-plot_features.py -f one --feature_name <span class="token string">&#34;Bacteria.Bacteroidetes&#34;</span> hmp_aerobiosis_small.in hmp_aerobiosis_small.res Bacteroidetes.png

<span class="token comment"># 差异特征</span>
lefse-plot_features.py -f <span class="token function">diff</span> --archive <span class="token function">zip</span> hmp_aerobiosis_small.in hmp_aerobiosis_small.res biomarkers.zip
</code></pre> 
<p>详细参数&#xff1a;</p> 
<pre><code class="prism language-shell">usage: lefse-plot_features.py <span class="token punctuation">[</span>-h<span class="token punctuation">]</span> <span class="token punctuation">[</span>--width WIDTH<span class="token punctuation">]</span> <span class="token punctuation">[</span>--height HEIGHT<span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--top TOP<span class="token punctuation">]</span> <span class="token punctuation">[</span>--bot BOT<span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--title_font_size TITLE_FONT_SIZE<span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--class_font_size CLASS_FONT_SIZE<span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--class_label_pos <span class="token punctuation">{<!-- --></span>up,down<span class="token punctuation">}</span><span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--subcl_mean <span class="token punctuation">{<!-- --></span>y,n<span class="token punctuation">}</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>--subcl_median <span class="token punctuation">{<!-- --></span>y,n<span class="token punctuation">}</span><span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--font_size FONT_SIZE<span class="token punctuation">]</span> <span class="token punctuation">[</span>-n flt<span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--format <span class="token punctuation">{<!-- --></span>png,pdf,svg<span class="token punctuation">}</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>-f <span class="token punctuation">{<!-- --></span>all,diff,one<span class="token punctuation">}</span><span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--feature_name FEATURE_NAME<span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--feature_num FEATURE_NUM<span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--archive <span class="token punctuation">{<!-- --></span>zip,none<span class="token punctuation">}</span><span class="token punctuation">]</span>
                              <span class="token punctuation">[</span>--background_color <span class="token punctuation">{<!-- --></span>k,w<span class="token punctuation">}</span><span class="token punctuation">]</span> <span class="token punctuation">[</span>--dpi DPI<span class="token punctuation">]</span>
                              INPUT_FILE INPUT_FILE OUTPUT_FILE

Cladoplot

positional arguments:
  INPUT_FILE            dataset files
  INPUT_FILE            LEfSe output <span class="token function">file</span>
  OUTPUT_FILE           the <span class="token function">file</span> <span class="token keyword">for</span> the output <span class="token punctuation">(</span>the <span class="token function">zip</span> <span class="token function">file</span> <span class="token keyword">if</span> an archive is
                        required, the output directory otherwise<span class="token punctuation">)</span>

optional arguments:
  -h, --help            show this <span class="token function">help</span> message and <span class="token keyword">exit</span>
  --width WIDTH
  --height HEIGHT
  --top TOP             <span class="token keyword">set</span> maximum y limit <span class="token punctuation">(</span>-1.0 means automatic limit<span class="token punctuation">)</span>
  --bot BOT             <span class="token keyword">set</span> minimum y limit <span class="token punctuation">(</span>default 0.0, -1.0 means automatic
                        limit<span class="token punctuation">)</span>
  --title_font_size TITLE_FONT_SIZE
  --class_font_size CLASS_FONT_SIZE
  --class_label_pos <span class="token punctuation">{<!-- --></span>up,down<span class="token punctuation">}</span>
  --subcl_mean <span class="token punctuation">{<!-- --></span>y,n<span class="token punctuation">}</span>
  --subcl_median <span class="token punctuation">{<!-- --></span>y,n<span class="token punctuation">}</span>
  --font_size FONT_SIZE
  -n flt                unused
  --format <span class="token punctuation">{<!-- --></span>png,pdf,svg<span class="token punctuation">}</span>
                        the <span class="token function">format</span> <span class="token keyword">for</span> the output <span class="token function">file</span>
  -f <span class="token punctuation">{<!-- --></span>all,diff,one<span class="token punctuation">}</span>     wheter to plot all features <span class="token punctuation">(</span>all<span class="token punctuation">)</span>, only those
                        differentially abundant according to LEfSe or only one
                        <span class="token punctuation">(</span>the one given with --feature_name<span class="token punctuation">)</span>
  --feature_name FEATURE_NAME
                        The name of the feature to plot <span class="token punctuation">(</span>levels separated by
                        .<span class="token punctuation">)</span>
  --feature_num FEATURE_NUM
                        The number of the feature to plot
  --archive <span class="token punctuation">{<!-- --></span>zip,none<span class="token punctuation">}</span>
  --background_color <span class="token punctuation">{<!-- --></span>k,w<span class="token punctuation">}</span>
                        <span class="token keyword">set</span> the color of the background
  --dpi DPI


</code></pre> 
<h3><a id="_380"></a>绘制系统发育树图</h3> 
<p>可以将差异结果&#xff0c;结合物种进化关系&#xff0c;绘制系统发育树图。前提是输入文件必须指定物种所有的物种等级。例如metaphlan的输出结果。如果物种太多&#xff0c;可以进一步对差异分析结果进行筛选过滤&#xff0c;只对差异特征进行绘图。</p> 
<pre><code class="prism language-shell"><span class="token comment">## 可直接绘制单个水平的图&#xff0c;也可将所有水平进行分析后&#xff0c;得到的结果进行绘图</span>
<span class="token comment">## 如果很多特征都是没有组间差异的&#xff0c;可以对特征进行筛选后再绘图 grep -v &#39;-&#39; 即可</span>
<span class="token comment">## --clade_sep 默认为1.5&#xff0c;但绘图时会自动调整&#xff0c;也可以自己设定</span>
<span class="token comment">## --abrv_stop_lev 7 默认为5&#xff0c;即展示到第5水平&#xff0c;可设置到7&#xff0c;暂时到第7水平的结果。可以结合标签参数和缩写参数来展示。</span>
lefse-plot_cladogram.py --dpi 500 all_level_lefse_significant.res all_level_lefse_significant_cladogram.pdf --format pdf --clade_sep 0.05 --abrv_stop_lev 7
</code></pre> 
<p>详细参数&#xff1a;</p> 
<pre><code class="prism language-shell">usage: lefse-plot_cladogram.py <span class="token punctuation">[</span>-h<span class="token punctuation">]</span> <span class="token punctuation">[</span>--clade_sep CLADE_SEP<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--max_lev MAX_LEV<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--max_point_size MAX_POINT_SIZE<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--min_point_size MIN_POINT_SIZE<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--point_edge_width MARKEREDGEWIDTH<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--siblings_connector_width SIBLINGS_CONNECTOR_WIDTH<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--parents_connector_width PARENTS_CONNECTOR_WIDTH<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--radial_start_lev RADIAL_START_LEV<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--labeled_start_lev LABELED_START_LEV<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--labeled_stop_lev LABELED_STOP_LEV<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--abrv_start_lev ABRV_START_LEV<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--abrv_stop_lev ABRV_STOP_LEV<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--expand_void_lev EXPAND_VOID_LEV<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--class_legend_vis CLASS_LEGEND_VIS<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--colored_connector COLORED_CONNECTORS<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--alpha ALPHA<span class="token punctuation">]</span> <span class="token punctuation">[</span>--title TITLE<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--sub_clade SUB_CLADE<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--title_font_size TITLE_FONT_SIZE<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--right_space_prop R_PROP<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--left_space_prop L_PROP<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--label_font_size LABEL_FONT_SIZE<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--background_color <span class="token punctuation">{<!-- --></span>k,w<span class="token punctuation">}</span><span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--colored_labels <span class="token punctuation">{<!-- --></span>0,1<span class="token punctuation">}</span><span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--class_legend_font_size CLASS_LEGEND_FONT_SIZE<span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--dpi DPI<span class="token punctuation">]</span> <span class="token punctuation">[</span>--format <span class="token punctuation">{<!-- --></span>png,svg,pdf<span class="token punctuation">}</span><span class="token punctuation">]</span>
                               <span class="token punctuation">[</span>--all_feats ALL_FEATS<span class="token punctuation">]</span>
                               INPUT_FILE OUTPUT_FILE

Cladoplot

positional arguments:
  INPUT_FILE            tab delimited input <span class="token function">file</span>
  OUTPUT_FILE           the <span class="token function">file</span> <span class="token keyword">for</span> the output image

optional arguments:
  -h, --help            show this <span class="token function">help</span> message and <span class="token keyword">exit</span>
  --clade_sep CLADE_SEP
  --max_lev MAX_LEV
  --max_point_size MAX_POINT_SIZE
  --min_point_size MIN_POINT_SIZE
  --point_edge_width MARKEREDGEWIDTH
  --siblings_connector_width SIBLINGS_CONNECTOR_WIDTH
  --parents_connector_width PARENTS_CONNECTOR_WIDTH
  --radial_start_lev RADIAL_START_LEV
  --labeled_start_lev LABELED_START_LEV
  --labeled_stop_lev LABELED_STOP_LEV
  --abrv_start_lev ABRV_START_LEV
  --abrv_stop_lev ABRV_STOP_LEV
  --expand_void_lev EXPAND_VOID_LEV
  --class_legend_vis CLASS_LEGEND_VIS
  --colored_connector COLORED_CONNECTORS
  --alpha ALPHA
  --title TITLE
  --sub_clade SUB_CLADE
  --title_font_size TITLE_FONT_SIZE
  --right_space_prop R_PROP
  --left_space_prop L_PROP
  --label_font_size LABEL_FONT_SIZE
  --background_color <span class="token punctuation">{<!-- --></span>k,w<span class="token punctuation">}</span>
                        <span class="token keyword">set</span> the color of the background
  --colored_labels <span class="token punctuation">{<!-- --></span>0,1<span class="token punctuation">}</span>
                        draw the label with class color <span class="token punctuation">(</span>1<span class="token punctuation">)</span> or <span class="token keyword">in</span> black <span class="token punctuation">(</span>0<span class="token punctuation">)</span>
  --class_legend_font_size CLASS_LEGEND_FONT_SIZE
  --dpi DPI
  --format <span class="token punctuation">{<!-- --></span>png,svg,pdf<span class="token punctuation">}</span>
                        the <span class="token function">format</span> <span class="token keyword">for</span> the output <span class="token function">file</span>
  --all_feats ALL_FEATS

</code></pre> 
<h2><a id="_462"></a>参考资料</h2> 
<p><a href="https://github.com/SegataLab/lefse">https://github.com/SegataLab/lefse</a></p>
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如何简化美化<em>LEfSe</em><em>分析</em>结果中的Cladogram图
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和C语言一样，Python也具有全局变量，其定义全局变量的用法有两种：

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便捷的方法时：

打开我们的cmd命令

输入Python

输入 import sys

输入 print(sys.path)

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1.默认路径是否个人的mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases（软件下载也是下载到这个路径）；
2.文件解压后是否在默认路径中（具体的数据库文件不需要解压）；
3.file_list.txt文件是否在默认路径中；
4.数据库文件是否受损（MD5校验一下）；
5.如果上面都没有问题，那得检查一下bowtie2是否安装成功。</span>
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